| Previous changeset 4:051953328516 (2020-11-27) Next changeset 6:948fc0276b4f (2024-03-02) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a" |
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modified:
seurat_find_variable_genes.xml seurat_macros.xml |
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added:
get_test_data.sh |
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| diff -r 051953328516 -r 5be60722113a get_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_test_data.sh Fri Mar 04 07:26:36 2022 +0000 |
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| @@ -0,0 +1,51 @@ +#!/usr/bin/env bash + +BASENAME_FILE='E-MTAB-6077-3k_features_90_cells' + +MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23' +RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n' +NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU' +FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ' +SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0' +PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c' +NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX' +CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa' +TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO' +MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD' + +LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX' +H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz' +SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe' + +function get_data { + local link=$1 + local fname=$2 + + if [ ! -f $fname ]; then + echo "$fname not available locally, downloading.." + wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link + fi +} + +# get matrix data +pushd test-data +get_data $MTX_LINK mtx.zip +unzip mtx.zip +rm -f mtx.zip + +get_data $RDS_LINK $BASENAME_FILE".rds" +get_data $NORM_LINK $BASENAME_FILE"-normalised.rds" +get_data $FVG_LINK $BASENAME_FILE"-fvg.rds" +get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds" +get_data $PCA_LINK $BASENAME_FILE"-pca.rds" +get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds" +get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds" +get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds" +get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip" + +unzip $BASENAME_FILE"-markers.csv.zip" +rm -f $BASENAME_FILE"-markers.csv.zip" + +get_data $LOOM_LINK $BASENAME_FILE"_loom.h5" +get_data $SCE_LINK $BASENAME_FILE"_sce.rds" +get_data $H5AD_LINK $BASENAME_FILE".h5ad" |
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| diff -r 051953328516 -r 5be60722113a seurat_find_variable_genes.xml --- a/seurat_find_variable_genes.xml Fri Nov 27 13:48:35 2020 +0000 +++ b/seurat_find_variable_genes.xml Fri Mar 04 07:26:36 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="seurat_find_variable_genes" name="Seurat FindVariableGenes" version="@SEURAT_VERSION@+galaxy0"> +<tool id="seurat_find_variable_genes" name="Seurat FindVariableGenes" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> <description>identify variable genes</description> <macros> <import>seurat_macros.xml</import> @@ -58,9 +58,12 @@ <tests> <test> - <param name="rds_seurat_file" ftype="rdata" value="normalised_seurat.rds"/> - <output name="rds_seurat_file" ftype="rdata" value="variable_genes_seurat.rds" compare="sim_size" delta="1000000" /> - <output name="output_tab" value="filtered_genes.txt" compare="sim_size" delta="1000000" /> + <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-normalised.rds"/> + <output name="rds_seurat_file" ftype="rdata"> + <assert_contents> + <has_size value="2720178" delta="200000"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ |
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| diff -r 051953328516 -r 5be60722113a seurat_macros.xml --- a/seurat_macros.xml Fri Nov 27 13:48:35 2020 +0000 +++ b/seurat_macros.xml Fri Mar 04 07:26:36 2022 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0.0.8</token> - <token name="@SEURAT_VERSION@">3.1.2</token> + <token name="@VERSION@">0.3.0</token> + <token name="@SEURAT_VERSION@">3.2.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">seurat-scripts</requirement> @@ -96,7 +96,10 @@ <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** -3.1.2_0.0.8: Upd ate metadata parsing + +3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support. + +3.1.2_0.0.8: Update metadata parsing 3.1.1_0.0.7: Exposes perplexity and enables tab input. @@ -105,9 +108,9 @@ Find clusters: removed dims-use, k-param, prune-snn. 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at -EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l). +EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l). -0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. +0.0.1: Initial contribution. Maria Doyle (github.com/mblue9). ]]></token> @@ -124,7 +127,7 @@ url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, } </citation> - <citation type="doi">10.1101/2020.04.08.032698</citation> + <citation type="doi">10.1038/s41592-021-01102-w</citation> </citations> </xml> </macros> |